A "rough" surface could mean many different things. You will have to clarify what kind of rough surface you want.
In nature, rough surfaces are created by a physical process(eg, deposition, aggregation, erosion...). If you want to create a realistically rough surface, then you may need to learn more about this process and simulate it. In that case, starting with a smooth spherical structure is probably good enough.
Generally speaking, when trying to create a system with a complicated geometry, most people do not rely on LAMMPS input script commands. Instead, they create a "DATA" file. The basic format of this file is explained here:
... and there are some tools to help you create these files here: